Workflow Entry: AffyArrayQualityAnalysis

The AffyArrayQualityAnalysis web services provide quality control for raw Affymetrix GeneChip data. They are wrappers around Philip de Groot's quality control R script to provide remote programmatic access. This example workflow demonstrates the use of the AffyArrayQualityAnalysis services. The flow is as follows:

• A client executes the AffyArrayQualityAnalysis_submit service with two inputs: a User object and a collection of URLs linking to CEL files.
• The User object contains a user ID, a password and an e-mail address. Currently the user ID and password can be any characters [a-zA-Z0-9]. Just pick something, there's no need to register them first. They are only used to make sure that the one who tries to download the results is the same person as the one who submitted the job.
• Your job will be submitted to the SUN Grid Engine on the NuGO R-server. The e-mail address is used by the Sun Grid Engine to notify you when your job is done. We might also use it to send you feedback in case something goes wrong with your job, but it won't be used for anything else and will only be stored for a maximum of 7 days (together with your job's results).
• The URLs to the CEL files must use either the http or https protocol. You can restrict access to these URLs using basic authentication and putting the username and password in the URL. For example if the user is pieter and the password is test you could have a URL like this: https://pieter:test@lab5.bioinformatics.nl/phenolink/home/TisMix_mix5a_01_v1_U133plus2.CEL. Hence you have to put the CEL files somewhere on a web server, so the AffyArrayQualityAnalysis_submit service can download them.
• The AffyArrayQualityAnalysis_submit service returns a job ID and a link to the results. Once the job is done this link can be used to download the results. Results will be available for 7 days after which they will be deleted automatically.
• The job ID is used to execute the AffyArrayQualityAnalysis_poll service inside a nested workflow. AffyArrayQualityAnalysis_poll returns the job status and unless the status is "finished" the entire nested workflow will fail. If the nested CheckStatus workflow fails, Taverna will automatically retry until it succeeds and hence the job has finished (or until the maximum number of retries is reached).
• The nested DownloadFile workflow depends on successful completion of the nested CheckStatus workflow. The name says it all: It downloads the result, which is a single ZIP file. This workflow does not take care of unzipping the archive. You have to do that yourself.

AffyArrayQualityAnalysis uses a secure connection over HTTPS. To make this work you *must* import our SSL certificates in your local Java keystores. You can do this either manually as described at https://www.bioinformatics.nl/phenolink/home/JavaAndHTTPS.html or use a Java tool to do the job as described at http://www.myexperiment.org/files/148